The elemental composition of the presynaptic and postsynaptic nerve terminals of rapidly-frozen synapses of the mouse cerebellar molecular layer was determined using electron probe x-ray microanalysis and elemental imaging by characteristic x-rays. Quantitative electron probe analysis of synaptic vesicle clusters and intraterminal mitochondria indicated that their calcium concentrations were 0.4 plus/minus 0.1 and 1.2 plus/minus 0.2 mmol/1 respectively. Similar experiments were carried out on cerebellar slices rapidly frozen after incubation in vitro. The distribution of K and Ca in presynaptic terminals of resting and depolarized slices were qualitatively and quantitatively similar to those in fresh slices. Results suggest that the vesicles have a limited role in calcium storage and release. In contrast measurement of calcium in the postsynaptic region of the cerebellar molecular layer show evidence for calcium sequestration in a smooth membrane cistern of the derdritic process called the "spine".